7SK6: Human ACKR3

Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ and an intracellular Fab. Determined by electron microscopy at 4.0 Å resolution. Released 27 Jul 2022.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,682
Mol. weight: 102.24 kDa
Released: 27 Jul 2022

Explore 7SK6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SK6 contains 19 α-helices and 37 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	1
α-helix	35-37	3
α-helix	40-75	36
β-strand	78-79	2	2
α-helix	81-95	15
α-helix	97-105	9
β-strand	109	1	3
α-helix	114-147	34
α-helix	154-181	28
β-strand	185	1	4
β-strand	195	1	3
β-strand	196	1	4
α-helix	205-217	13
α-helix	218-222	5
α-helix	223-241	19
α-helix	245-248	4
α-helix	252-279	28
α-helix	287-312	26
α-helix	313-317	5
α-helix	320-330	11

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	15	1	5
β-strand	26-30	5	1
β-strand	36-41	6	1
β-strand	48-49	2	1
β-strand	51	1	5
α-helix	56-64	9

Chain E: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
β-strand	20-26	7	6
β-strand	34-35	2	7
β-strand	36-38	3	8
β-strand	39	1	9
β-strand	46-50	5	8
β-strand	54-55	2	8
α-helix	56	1
β-strand	63-66	4	6
β-strand	72-76	5	6
β-strand	86	1	9
β-strand	87	1	10
β-strand	90-91	2	7
α-helix	97	1
β-strand	98-99	2	7
β-strand	103	1	10

Chain F: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	11
β-strand	13-14	2	12
β-strand	20-28	9	11
β-strand	36-42	7	12
β-strand	48-55	8	12
β-strand	60-63	4	12
α-helix	65-67	3
β-strand	72-76	5	11
β-strand	81-87	7	11
β-strand	95-102	8	12
β-strand	111-112	2	2
β-strand	119-120	2	12
β-strand	124-127	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Atypical chemokine receptor 3	A	protein	393	Homo sapiens	P25106 (AlphaFold model)
Stromal cell-derived factor 1	B	protein	69	Homo sapiens	P48061 (AlphaFold model)
CID24 Fab light chain	E	protein	215	Homo sapiens
CID24 Fab heavy chain	F	protein	238	Homo sapiens

Sequence of entity 1 (A), FASTA

>7SK6_1 Atypical chemokine receptor 3 (chains A)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Sequence of entity 2 (B), FASTA

>7SK6_2 Stromal cell-derived factor 1 (chains B)
LRHQSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQ
EYLEKALNK

Sequence of entity 3 (E), FASTA

>7SK6_3 CID24 Fab light chain (chains E)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYYYPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (F), FASTA

>7SK6_4 CID24 Fab heavy chain (chains F)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISPSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVSYWDWTWGWSKYEGMDYW
GQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Primary citation

Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. Yen, Y.C., Schafer, C.T., Gustavsson, M. et al. Sci Adv (2022) 8:eabn8063-eabn8063. DOI 10.1126/sciadv.abn8063 · PubMed

Other PDB entries of the same protein (UniProt P25106 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6K3F 2.3 Å, Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide
8TII 3.0 Å, Human ACKR3 phosphorylated by GRK2 in complex with Arrestin2 in nanodisc
7SK4 3.3 Å, Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an…
7SK7 3.3 Å, Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial…
7SK8 3.3 Å, Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial…
8VJ9 3.3 Å, CryoEM structure of human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 variant…
9E82 3.4 Å, ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7
8TIO 3.6 Å, Human ACKR3 with C tail extended by 12 glycines phosphorylated by GRK5 in complex with…
7SK9 3.7 Å, Cryo-EM structure of human ACKR3 in complex with a small molecule partial agonist…
7SK3 3.8 Å, Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an…
8TIL 3.8 Å, Human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 reconstructed without…
7SK5 4.0 Å, Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab

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